prepareCHRannotation {goCluster} | R Documentation

## A function to prepare the gene localization for subsequent statistical analysis

### Description

This function builds an association table between a given list of genes and the chromosome they can be found on.

### Usage

    prepareCHRannotation(uniqueID, annBuilderPkg, chromosomes = NULL, trueID = NULL)

### Arguments

`uniqueID` | The unique ID that should be associated with the gene ontology annotation.
`annBuilderPkg` | The AnnBuilder package that provides the basis for retrieving the annotation information.
`chromosomes` | The output is restricted to genes lying on these chromosomes.
`trueID` | The true ID specifies the type of ID that the chromosome information has been linked to (e.g. Locus Link). If this ID differs from the the type of `uniqueID` this has to be specified so that the IDs are converted accordingly. The option needs to match the name of the AnnBuilder package environment (without the prefix) that provides the conversion information.

### Details

The class retrieves information about the chromosome each gene lies on from a given AnnBuilder annotation package and converts that information into a format useful for the subsequent analysis. The class removes all genes not present in the in the dataset, eliminates any duplicate entries (respecting the true ID if specified) and can remove any chromosomes that should not be included into analysis.

### Value

A composite list of the (possibly converted) unique ID and the association table.

`annotations` | The association table linking the genes with the chromosome they lie on.
`uniqueid` | Either a copy of the original unique identifiers or a converted copy that matches the original vector in length but specifies the new gene ID for each gene.

### Author(s)

Gunnar Wrobel, http://www.gunnarwrobel.de.

### See Also

`clusterAnnotationChromosome-abp-class`

### Examples

    prepareCHRannotation(c("YGL213C", "YGL215W", "YGL216W", "YGL218W",
    "YGL219C", "YGL220W", "YGL221C", "YGL222C", "YGL223C", "YGL224C",
    "YGL225W"), "YEAST")

[Package goCluster version 1.0.3 Index]